If you are planning to do major pruning then do it in late autumn or early winter when the trees go dormant. Late winter and early spring is the best time to prune apple fruit trees. This should be done before the new bud appear. Remove all the old, dead, diseased and damaged branches from the tree. Also remove the branches that are weak, cross each other or grow downward. Make all the cuts flush with the main branch without damaging the bark.